Little fan on mobo

Ok I've been having a lot of problems with my old pc. I can't remember all of the specs either but I'll fill you in as best I can. I've even read a few of the problems that other people have had and nothing works.

It started making a clicking noise from what sounded like the area where my two HD are and would then lock up for a few seconds. And then run fine for about 1-1.5 hours then do it again. I thought that it may have been the HD itself so I put in a good 80gb that I had. Everything worked fine for a few months and now its happening again only now it can't make it past the windows start up screen or if it does it goes it the screen that it checks the HD for errors at and freezes there.

So I pull the side off a few minutes ago and turn it on to watch my fans. All are working but that tiny fan on the mobo itself. Could this have been the problem? To me it doesn't seam likely but I'm not an ace at this but not a total noob either. All of the connections to every bit of removable add-ons were seated firmly. I'm lost now and don't have a clue as to what to do next. :dead:

Thank you all for any help that you may be able to give!

:edit: I turned the old PC on and took it to bios. I let it run for about 10 minutes and the temp went to 147F. I've never had problams with the temp before all of this started happening.